Identification of novel biomass-degrading enzymes from genomic dark matter: Populating genomic sequence space with functional annotation.

Although recent nucleotide sequencing technologies have significantly enhanced our understanding of microbial genomes, the function of ∼35% of genes identified in a genome currently remains unknown. To improve the understanding of microbial genomes and consequently of microbial processes it will be crucial to assign a function to this "genomic dark matter." Due to the urgent need for additional carbohydrate-active enzymes for improved production of transportation fuels from lignocellulosic biomass, we screened the genomes of more than 5,500 microorganisms for hypothetical proteins that are located in the proximity of already known cellulases. We identified, synthesized and expressed a total of 17 putative cellulase genes with insufficient sequence similarity to currently known cellulases to be identified as such using traditional sequence annotation techniques that rely on significant sequence similarity. The recombinant proteins of the newly identified putative cellulases were subjected to enzymatic activity assays to verify their hydrolytic activity towards cellulose and lignocellulosic biomass. Eleven (65%) of the tested enzymes had significant activity towards at least one of the substrates. This high success rate highlights that a gene context-based approach can be used to assign function to genes that are otherwise categorized as "genomic dark matter" and to identify biomass-degrading enzymes that have little sequence similarity to already known cellulases. The ability to assign function to genes that have no related sequence representatives with functional annotation will be important to enhance our understanding of microbial processes and to identify microbial proteins for a wide range of applications.

The protective effect of ascorbic acid derivative on PC12 cells: involvement of its ROS scavenging ability.

L-ascorbic acid 2-phosphate-6-palmitate (Asc2P6P) was synthesized and its effect on the damage of PC12 cells induced by H2O2 was investigated. 200 microM H2O2 in a treatment period of 4 hours in our experiment resulted in substantial cell loss. With the increasing concentration of antioxidants, such H2O2-induced cytotoxicity was significantly prevented and the corresponding intracellular and extracellular ROS levels decreased concurrently by pre-treatment with Asc2P6P and Asc. It was found that Asc2P6P was superior to L-ascorbic acid in its protective role and showed a dose-dependent manner during a 24-hour treatment. The higher potency of Asc2P6P's protective role on PC12 cells was correlated with its more effective ROS scavenging ability. HPLC assay demonstrated that Asc2P6P could easily enter the cells and be converted into Asc persistently, which contributed to its distinguished role in protecting PC12 cells against H2O2-induced cytotoxicity.

Neuroprotective effects of Hypericum perforatum on trauma induced by hydrogen peroxide in PC12 cells.

The standard extracts of Hypericum perforatum L. (SEHP), a well-known medicinal plant, are used for the treatment of depression, exhibited upgrading and significant protective effects on the trauma of PC12 cells induced by 200 microM H2O2 in a dose-dependent manner within 24-hour treatment. Cell viability was assessed by the MTT method, and in situ cellular hydrogen peroxide (H2O2)-induced oxidative stress was examined by measurement of reactive oxygen species (ROS) formation using CDCFH procedures. Intra- and extra-cellular ROS levels decreased significantly to 71.9% and 50.0% of the control at a moderate concentration of 20 microg/ml, respectively, suggesting that SEHP could easily enter the cells and play important roles in reducing ROS levels. Our results were proved by detection of DNA fragmentation and inspection of cell morphology of PC12 cells. SEHP can obviously block DNA fragmentation and prevent the cells from shrinking and turning round of H2O2-induced apoptosis in PC12 cells at concentrations of 10 approximately 100 microg/ml. This data suggests SEHP may be a candidate for application in neurodegenerative diseases such as Alzheimer's disease or Parkinson's disease.

[Protective effects of Cleistocalyx operculatus on lipid peroxidation and trauma of neuronal cells].

OBJECTIVE: To observe the protective effects of Cleistocalyx operculatus on lipid peroxidation in rat liver microsomes and on the trauma of PC12 cells induced by H2O2. METHOD: The mouse liver homogenate lipid peroxidation assay and PC12 Cell culture and Cell viability (MTT assay) were applied. RESULT: Cleistocalyx operculatus showed strong protective effects on lipid peroxidation in rat liver microsomes in a dose-dependent manner and exhibited potent protective effects on the trauma of PC12 cells induced by H2O2 (200 micromol x L(-1)) when the concentration reached 1.00 g x L(-1). CONCLUSION: Cleistocalyx operculatus may be used as antioxidant to prevent or delay the pathogenesis of neural cell diseases.

Extracellular superoxide dismutase suppresses hypoxia-inducible factor-1α in pancreatic cancer.

Hypoxia-inducible factor-1 (HIF-1) is a heterodimeric transcription factor that governs cellular responses to reduced oxygen availability by mediating crucial homeostatic processes and is a major survival determinant for tumor cells growing in a low-oxygen environment. Clinically, HIF-1α seems to be important in pancreatic cancer, as HIF-1α correlates with metastatic status of the tumor. Extracellular superoxide dismutase (EcSOD) inhibits pancreatic cancer cell growth by scavenging nonmitochondrial superoxide. We hypothesized that EcSOD overexpression leads to changes in the O2(-)/H2O2 balance modulating the redox status affecting signal transduction pathways. Both transient and stable overexpression of EcSOD suppressed the hypoxic accumulation of HIF-1α in human pancreatic cancer cells. This suppression of HIF-1α had a strong inverse correlation with levels of EcSOD protein. Coexpression of the hydrogen peroxide-removing protein glutathione peroxidase did not prevent the EcSOD-induced suppression of HIF-1α, suggesting that the degradation of HIF-1α observed with high EcSOD overexpression is possibly due to a low steady-state level of superoxide. Hypoxic induction of vascular endothelial growth factor (VEGF) was also suppressed with increased EcSOD. Intratumoral injections of an adenoviral vector containing the EcSOD gene into preestablished pancreatic tumors suppressed both VEGF levels and tumor growth. These results demonstrate that the transcription factor HIF-1α and its important gene target VEGF can be modulated by the antioxidant enzyme EcSOD.

Mechanisms of ascorbate-induced cytotoxicity in pancreatic cancer.

PURPOSE: Pharmacologic concentrations of ascorbate may be effective in cancer therapeutics. We hypothesized that ascorbate concentrations achievable with i.v. dosing would be cytotoxic in pancreatic cancer for which the 5-year survival is <3%. EXPERIMENTAL DESIGN: Pancreatic cancer cell lines were treated with ascorbate (0, 5, or 10 mmol/L) for 1 hour, then viability and clonogenic survival were determined. Pancreatic tumor cells were delivered s.c. into the flank region of nude mice and allowed to grow at which time they were randomized to receive either ascorbate (4 g/kg) or osmotically equivalent saline (1 mol/L) i.p. for 2 weeks. RESULTS: There was a time- and dose-dependent increase in measured H(2)O(2) production with increased concentrations of ascorbate. Ascorbate decreased viability in all pancreatic cancer cell lines but had no effect on an immortalized pancreatic ductal epithelial cell line. Ascorbate decreased clonogenic survival of the pancreatic cancer cell lines, which was reversed by treatment of cells with scavengers of H(2)O(2). Treatment with ascorbate induced a caspase-independent cell death that was associated with autophagy. In vivo, treatment with ascorbate inhibited tumor growth and prolonged survival. CONCLUSIONS: These results show that pharmacologic doses of ascorbate, easily achievable in humans, may have potential for therapy in pancreatic cancer.

Mitochondrial ROS and radiation induced transformation in mouse embryonic fibroblasts.

Manganese superoxide dismutase (SOD2) is a nuclear encoded and mitochondria localized antioxidant enzyme that converts mitochondria derived superoxide to hydrogen peroxide. This study investigates the hypothesis that mitochondria derived reactive oxygen species (ROS) regulate ionizing radiation (IR) induced transformation in normal cells. Mouse embryonic fibroblasts (MEFs) with wild type SOD2 (+/+), heterozygous SOD2 (+/-), and homozygous SOD2 (-/-) genotypes were irradiated with equitoxic doses of IR, and assayed for transformation frequency, cellular redox environment, DNA damage, and cell cycle checkpoint activation. Transformation frequency increased ( approximately 5-fold) in SOD2 (-/-) compared to SOD2 (+/+) MEFs. Cellular redox environment (GSH, GSSG, DHE and DCFH-oxidation) did not show any significant change within 24 h post-IR. However, a significant increase in cellular ROS levels was observed at 72 h post-IR in SOD2 (-/-) compared to SOD2 (+/+) MEFs, which was consistent with an increase in GSSG in SOD2 (-/-) MEFs. Late ROS accumulation was associated with an increase in micronuclei frequency in SOD2 (-/-) MEFs. Exit from G(2) was accelerated in irradiated SOD2 (+/-) and SOD2 (-/-) compared to SOD2 (+/+) MEFs. These results support the hypothesis that SOD2 activity and mitochondria generated ROS regulate IR induced transformation in mouse embryonic fibroblasts.

Enhancement of fibrinolytic activity of bovine aortic endothelial cells by ginsenoside Rb2.

AIM: The effect of ginsenoside Rb2 purified from Panax ginseng on fibrinolytic activity of bovine aortic endothelial cells (BAEC) was investigated. METHODS: Cellular plasminogen activator (PA) level of the lysates was measured by the chromogenic substrate S-2403. Fibrin underlay technique was carried out to observe fibrinolysis by growing endothelial cells in the culture medium. Cell viability was then determined by measurement of the activity of mitochondrial dehydrogenase. The ability of Rb2 of potentiating cellular PA activity was investigated by measuring the amounts of PA and PA inhibitor-1 (PAI-1) in the culture medium using zymography and reverse zymography. Changes in the expression of urokinase-type PA (uPA), uPA receptor, and PAI-1 mRNA in BAEC after treatment with Rb2 were analyzed by Northern blot. RESULTS: Rb2 enhanced cellular PA activity in a concentration-and time-dependent manner. Treatment of BAEC with Rb2 10 mg/L for 9 h resulted in a 3.5-fold increase of PA activity without a marked cytotoxic effect, as shown by LDH levels in culture. Increased PA levels caused the increase in surface plasmin levels as observed by fibrin underlay technique. Rb2 greatly or moderately increased the amount of urokinase-type PA (uPA) or its inhibitor (PAI-1), present in the culture medium, whereas saponin did not influence mRNA levels of uPA, its surface receptor, and PAI-1, suggesting that Rb2 may stimulate the secretion of uPA without enhancing its gene expression. The enhancement of PA levels by retinoic acid alone, a stimulator of PA synthesis, was potentiated by the simultaneous addition of ginsenoside Rb2 1 mg/L. Therefore, Rb2 might exert a strong synergism in the synthesis of cellular PA in BAEC. CONCLUSION: Ginsenoside Rb2 enhanced the PA activity levels in BAEC as well as the surface plasmin activity of BAEC. Rb2 may stimulate the secretion of uPA without enhancing the gene expression of uPA, uPA receptor (uPAR), and PAI-1.